Ok, in the days of Archer and the NX, im asuming there isnt a lot of deep space mining capabilities and that most of the resources used to build that eras starships come from Earth itself, or the moon.

I was toying with the idea of leaving out the orbital mining facility and mining facility in this era, and giving sufficient starting resources to get through this era until these facilites become available in the TMP era....

Not a bad idea, but wouldn't they have them before the TMP era even before the TOS era. The federation had been around for 100 years by the time Kirk took command of the 1701. I'd make them available as the Federation is founded.

what about a when you colonize a planet don't have an orbital mining facility just include say a build option in the planet properties to build a mining facility then research an upgrade that will produce a facility in space.

Hey in the Federations time line they found the resources needed for warp on jupiter/mars ( cant remember which 1 , they found the crystals before the the first warp flight ) . and i agree with both methods of mining ( Planet born base and a deep space 1 ) .